Wang Xiaohan, Choi Yu-Mi, Jeon Young-Ah, Yi JungYoon, Shin Myoung-Jae, Desta Kebede Taye, Yoon Hyemyeong
National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea.
Plants (Basel). 2023 Dec 13;12(24):4154. doi: 10.3390/plants12244154.
Adzuki beans are widely cultivated in East Asia and are one of the earliest domesticated crops. In order to gain a deeper understanding of the genetic diversity and domestication history of adzuki beans, we conducted Genotyping by Sequencing (GBS) analysis on 366 landraces originating from Korea, China, and Japan, resulting in 6586 single-nucleotide polymorphisms (SNPs). Population structure analysis divided these 366 landraces into three subpopulations. These three subpopulations exhibited distinctive distributions, suggesting that they underwent extended domestication processes in their respective regions of origin. Phenotypic variance analysis of the three subpopulations indicated that the Korean-domesticated subpopulation exhibited significantly higher 100-seed weights, the Japanese-domesticated subpopulation showed significantly higher numbers of grains per pod, and the Chinese-domesticated subpopulation displayed significantly higher numbers of pods per plant. We speculate that these differences in yield-related traits may be attributed to varying emphases placed by early breeders in these regions on the selection of traits related to yield. A large number of genes related to biotic/abiotic stress resistance and defense were found in most quantitative trait locus (QTL) for yield-related traits using genome-wide association studies (GWAS). Genomic sliding window analysis of Tajima's D and a genetic differentiation coefficient (Fst) revealed distinct domestication selection signatures and genotype variations on these QTLs within each subpopulation. These findings indicate that each subpopulation would have been subjected to varied biotic/abiotic stress events in different origins, of which these stress events have caused balancing selection differences in the QTL of each subpopulation. In these balancing selections, plants tend to select genotypes with strong resistance under biotic/abiotic stress, but reduce the frequency of high-yield genotypes to varying degrees. These biotic/abiotic stressors impact crop yield and may even lead to selection purging, resulting in the loss of several high-yielding genotypes among landraces. However, this also fuels the flow of crop germplasms. Overall, balancing selection appears to have a more significant impact on the three yield-related traits compared to breeder-driven domestication selection. These findings are crucial for understanding the impact of domestication selection history on landraces and yield-related traits, aiding in the improvement of adzuki bean varieties.
小豆在东亚广泛种植，是最早被驯化的作物之一。为了更深入地了解小豆的遗传多样性和驯化历史，我们对来自韩国、中国和日本的366个地方品种进行了简化基因组测序（GBS）分析，共获得6586个单核苷酸多态性（SNP）位点。群体结构分析将这366个地方品种分为三个亚群。这三个亚群呈现出独特的分布，表明它们在各自的起源地经历了漫长的驯化过程。对这三个亚群的表型变异分析表明，韩国驯化的亚群百粒重显著更高，日本驯化的亚群每荚粒数显著更多，中国驯化的亚群单株荚数显著更多。我们推测，这些产量相关性状的差异可能归因于这些地区早期育种者在产量相关性状选择上的不同侧重点。通过全基因组关联研究（GWAS）在大多数产量相关性状的数量性状位点（QTL）中发现了大量与生物/非生物胁迫抗性及防御相关的基因。对 Tajima's D 和遗传分化系数（Fst）的基因组滑动窗口分析揭示了每个亚群内这些QTL上独特的驯化选择特征和基因型变异。这些发现表明，每个亚群在不同的起源地经历了不同的生物/非生物胁迫事件，其中这些胁迫事件在每个亚群的QTL中导致了平衡选择差异。在这些平衡选择中，植物倾向于选择在生物/非生物胁迫下具有强抗性的基因型，但会不同程度地降低高产基因型的频率。这些生物/非生物胁迫因素影响作物产量，甚至可能导致选择清除，致使地方品种中一些高产基因型丢失。然而，这也促进了作物种质的流动。总体而言，与育种者驱动的驯化选择相比，平衡选择似乎对这三个产量相关性状有更显著的影响。这些发现对于理解驯化选择历史对地方品种和产量相关性状的影响至关重要，有助于小豆品种的改良。
